温馨提示×

温馨提示×

您好,登录后才能下订单哦!

密码登录×
登录注册×
其他方式登录
点击 登录注册 即表示同意《亿速云用户服务条款》

R语言的maf_oncoplot.r怎么使用

发布时间:2022-03-19 15:30:11 来源:亿速云 阅读:300 作者:iii 栏目:开发技术

本篇内容介绍了“R语言的maf_oncoplot.r怎么使用”的有关知识,在实际案例的操作过程中,不少人都会遇到这样的困境,接下来就让小编带领大家学习一下如何处理这些情况吧!希望大家仔细阅读,能够学有所成!

maf_oncoplot.r突变注释文件分类可视化maftools

使用方法:

Rscript /share/nas1/zhangll/MAF/code/maf_oncoplot.r -h
usage: /share/nas1/zhangll/MAF/code/maf_oncoplot.r [-h] -i maffile -m metadata
                                                   -g group
                                                   [-a additive [additive ...]]
                                                   [-T topgene]
                                                   [-l genelist [genelist ...]]
                                                   [-t] [-o outdir]
                                                   [-H height] [-W width]

Mutation annotation file classification
visualization:https://www.亿速云.com/article/1518

optional arguments:
  -h, --help            show this help message and exit
  -i maffile, --maf maffile
                        input the maf file[required]
  -m metadata, --meta metadata
                        input metadata file path[required]
  -g group, --group group
                        input group id in metadata file to classification
                        visualization[required]
  -a additive [additive ...], --additive additive [additive ...]
                        add additional class[optional,default: NULL]
  -T topgene, --top topgene
                        Number of top genes displayed [optional, default: 20]
  -l genelist [genelist ...], --genelist genelist [genelist ...]
                        the selected gene list to display [optional, default:
                        NULL]
  -t, --showtitle       whether show maftools title of plot [optional,
                        default: False]
  -o outdir, --outdir outdir
                        output file directory [default cwd]
  -H height, --height height
                        the height of pic inches [default 8]
  -W width, --width width
                        the width of pic inches [default 8]

参数说明:

-i   突变注释文件maf的路径,可从TCGA数据库中直接下载:


Hugo_Symbol

Entrez_Gene_Id

Center

NCBI_Build

Chromosome

Start_Position

End_Position

Strand

Variant_Classification

MFN2

9927

WUGSC
GRCh48
chr1

12001777
12001777

+

Missense_Mutation

KCNG3

170850

WUGSC
GRCh48
chr2

42444578
42444578
+Missense_Mutation



MAP2


4133
WUGSCGRCh48

chr2

209692762
209692762
+


Missense_Mutation

HEG1

57493

WUGSC
GRCh48

chr3

125010546
125010546
+

Missense_Mutation

PCDHB11

56125

WUGSC
GRCh48

chr5

141200541
141200541

+

Missense_Mutation

NSD1

64324

WUGSC
GRCh48

chr5

177294257
177294257

+

Missense_Mutation

F13A1

2162
WUGSCGRCh48

chr6


6174609
6174609

+

Missense_Mutation

PRRT4

401399

WUGSC
GRCh48

chr7

128359624
128359624

+

Missense_Mutation

FBP2

8789

WUGSC
GRCh48

chr9

94558941
94558941

+

Missense_Mutation

-m   metadata文件,病人样本的各种特征信息,必须包含以patient命名的患者TCGA编号列:


patient

sample

shortLetterCode

tumor_stage
tissue_or_organ_of_origin

alcohol_history

gender

ethnicity

race

TCGA-M9-A5M8

TCGA-M9-A5M8-01A

TP

stage iia

Lower third of esophagus

Yes

male

not reported

not reported

TCGA-R6-A6DQ

TCGA-R6-A6DQ-01B

TP

not reported


Lower third of esophagus

Yes

female

not hispanic or latino

white

TCGA-LN-A9FP

TCGA-LN-A9FP-01A

TP


stage iia
Middle third of esophagus

Yes

female

not hispanic or latino

asian

TCGA-LN-A4MQ

TCGA-LN-A4MQ-01A

TP

stage iii

Lower third of esophagus

No

male

not hispanic or latino

asian

TCGA-JY-A93D

TCGA-JY-A93D-01A

TP

stage iiic

Lower third of esophagus

Yes

male

not reported

white

TCGA-IG-A3YB

TCGA-IG-A3YB-01A

TP

stage iiia

Lower third of esophagus

No

male

not hispanic or latino

white

TCGA-IC-A6RF

TCGA-IC-A6RF-01A

TP

stage ia

Middle third of esophagus

Yes

female

not hispanic or latino

white

TCGA-VR-A8EX

TCGA-VR-A8EX-01A

TP

stage iva

Middle third of esophagus

No

male

not reported

not reported

-g   指定metadata 分组列名,如果分组名字有空格,应该用引号引起来

-a   附加分组列名,结果将在图中显示

-T   可指定所要展示的top基因个数,默认20

-l   可指定所要展示的基因列表,基因之间用空格隔开,默认NULL

使用举例:

Rscript  /share/nas1/zhangll/MAF/code/maf_oncoplot.r  -i /share/nas1/zhangll/MAF/TCGA-ESCA.maf_maftools.maf -m /share/nas1/huangls/project/TCGA_ESCA/metadata.tsv -g gender

“R语言的maf_oncoplot.r怎么使用”的内容就介绍到这里了,感谢大家的阅读。如果想了解更多行业相关的知识可以关注亿速云网站,小编将为大家输出更多高质量的实用文章!

向AI问一下细节

免责声明:本站发布的内容(图片、视频和文字)以原创、转载和分享为主,文章观点不代表本网站立场,如果涉及侵权请联系站长邮箱:is@yisu.com进行举报,并提供相关证据,一经查实,将立刻删除涉嫌侵权内容。

AI